PHREEQC Input

Fig. 30 Example for a PHREEQC input file (dissolution of the mineral rutherfordine as a function of the C02 partial pressure)...

Alternatively to the keyword SOLUTION, SOLUTIONSPREAD can be used for the input of solution. The input is transposed compared to the input for SOLUTION, i.e. the rows of input for SOLUTION become the columns of input for SOLUTION SPREAD. It is especially convenient to define more than one aqueous solution composition using this tab-limited format. Data obtained e g. from a laboratory spreadsheet format can be copied directly into the PHREEQC input file. SOLUTION SPREAD is compatible with the format of many spreadsheet programs, as e.g. Excel. The column headings are element names, element valence state names or isotope names. One subheading can be used to define speciation (e.g. as S04 , or as N03 ), specify element specific units, redox couples, phase names and saturation indices. All succeeding lines are the data values for each solution, with one solution defined on each line. 

When considering the increment of 1 for pE and pH, i.e. 15 pH values 31 pE values, the output file would comprise 465 jobs, numbered from SOLUTION 1 to SOLUTION 465, each containing different pE- and pH values. In fact, there will be only 377 jobs since the SOLUTIONS with pE-pH values above or below the stability field of water are missing. The water constituents defined under SOLUTION (e.g. Fe, Ca, Cl, C, S, etc.) are alike in all 377 jobs. Opening this input file takes about 30 seconds. Because files larger than 32 k cannot be opened in the Windows environment of PHREEQC either they have to be divided into smaller files or they have to be started directly with phreeqc.exe in the DOS prompt (phreeqc Input-File-Name Output-File-Name Database name). 

First of all both solutions, the acid mine water and the groundwater, are defined in the PHREEQC input file and mixed applying the keyword MIX. Then this solution is saved as solution 3 (SAVE SOLUTION) and the job is finished by END. A second job follows, which uses again SOLUTION 2 (groundwater) and SOLUTION 3 (1 1 diluted water) via the key word USE, once again mixes both solutions 1 1, and saves the result as SOLUTION 4, etc. SELECTED OUTPUT facilitates the further data processing in EXCEL by providing the pH values and the molalities of all uranium species. The key word itself has to be repeated for every job, as well as the definition of the desired parameters pH and molalities. 

To answer this question, the result of question 1 has to be saved in the PHREEQC input file with SAVE SOLUTION 3, called up in a new job by USE SOLUTION... 

Other examples of phreeqc input files will be discussed in later chapters. 

For example, here is a phreeqc input file which would give results very much like those of Figure 8.6 (which was actually created with The Geochemist s Workbench ). 

Table 8.1. phreeqc input file for titrating MW-36 with HCl. 

The phreeqc input file is shown in Table 8.1. Note that we use sulfate for charge balance, because it is the most abundant ion. The default definition of alkalinity in phreeqc is as calcite , which is what our analysis shows, so we simply enter that number (153 mg L-1). Under the keyword REACTION, a suitable combination of moles of HCl and number of steps is found with some calculation and a certain amount of trial and error. We specify the file name of the output file to ensure we get an output file with the essential data arranged for copying to a spreadsheet. The results are shown in Figure 8.2. 

Table 8.2. Titration of sample TS-3 with calcite. phreeqc input file.

Table 8.4. phreeqc input file for mixing fluids in a fertilizer problem. (Continued on next page.)... 

Table 10.1. (Continued from previous page). A modified phreeqc input file for Example 11 from Parkhurst and Appelo (1999). The modifications are shown as commented out (lines beginning with ). The results are shown in Figure 10.1.

Table 10.2. phreeqc input for a reactive transport model to simulate fluid pH buffering at the Bear Creek site. This is a better alternative to the titration model in described Chapter 8. 

Initial conditions were specified to reflect site conditions in 1994 when a major field sampling program took place (Zhu et al., 2002). The domain was divided into four zones (Figure 10.4), reflecting groundwater geochemical zonations observed in the field (Zhu et al., 2002). The pore fluid chemistry and aquifer mineral compositions for each zone are shown in the phreeqc input file (Table 10.3). 

In 1995 PHREEQC (Parkhurst 1995) was completely rewritten using the C programming language. This version removed nearly all limits regarding number of elements, aquatic species, solutions, phases, exchangers and surface complexes and caused the abolition of Fortran formats in the input files. Additionally, the equation solver was revised (more robust now) and several other options were added. With the 1995 version to the present, the following options have been possible ... 

Next, it will be shown how a simple input file looks like with PHREEQC and EQ 3/6 (Fig. 30 and Fig. 31) simulating the dissolution of the mineral rutherfordine in a water with 1 mmol/L sodium-chloride and low sulfate concentrations (0.0001 mmol/L) under oxidizing conditions (pE = 14) at 25 °C and at a C02 partial pressure of 0.033 kPa (atmospheric concentration). 

Here too, it is clearly visible that the definition of a problem is much more easily and quickly done with PHREEQC. A Windows user interface for PHREEQC, freely available by internet (http //www.geo.vu.nl/users/posv/phreeqc.html), simplifies the input even more. 

The file unpacks and installs itself independently and is started via PHREEQC.exe. After the start of the program, a window with four tab pages opens INPUT (chapter 2.2.1.1), DATABASE (chapter 2.2.1.2), GRID (chapter 2.2.1.4), and CHART (chapter 2.2.1.5). 

The input window consists of two windows. The left, initially blank window is the space to enter the chemical analysis to be modeled together with the commands to perform the particular modeling task. PHREEQC keywords and PHREEQC BASIC statements may be listed in the right window. A mouse click on the + symbol displays the list of keywords. The utilization of the BASIC commands is explained in chapter 2.2.2.22. 

A list of element concentrations follows. Whereas ions like Ca, Mg, etc. that occur only in one redox stage are indicated as elements, ions whose concentration is determined in different redox states are denoted individually with their valence in parentheses, as in the example of Fe3+ and Fe2+. However, the syntax is defined in the database (. dat) not in the PHREEQC code. For complexes like HC03", N03 S042, three input options exist ... 

As PHREEQC for Windows does not use an extension for saving (like e.g. .doc for word documents), it is advisable to either create an extension of one s own (e.g. phr ) or to save all input files in a separate directory. The input files are plain ASCII files that can be read and edited with any editor. 

To model balanced reactions, kinetics or reactive transports, more keywords besides TITLE, SOLUTION and END are needed, which will be listed in the following. Furthermore, the individual input parameters are described in detail in the PHREEQC manual. 

The modeling can be started either via Calculations/Start or by the icon pocket calculator . A PHREEQC for Windows-progress window opens showing input, output and data set file as well as the calculation progress in line 4. DONE appears when the calculation is performed or terminated. By clicking on DONE, the progress window closes and the output folder opens. 

In comparison to this calculation, the dissolution of gypsum in distilled water shall now be modeled by means of PHREEQC The input is very simple as it concerns distilled water and thus, the SOLUTION block contains only pH = 7 and temperature = 20 °C. To force equilibrium with gypsum, the keyword EQUILIBRIUMPHASES and the saturation index of 0 are used. 

In the next example the PHREEQC job is presented that simulates the experiment. To adjust the model to the data observed, the exchange capacity (X under EXCHANGE, here 0.0015 mol per kg water), the selectivity coefficients in the data set WATEQ4F.dat and the chosen dispersivity (TRANSPORT, dispersivity, here 0.1 m) are decisive besides the spatial discretisation (number of cells, here 40). If one sets the dispersivity to a very small value (e.g. T10"6) in the input file Exchange and rerun the job, one will see that no numerical dispersion occurs showing that numerical stability criteria are maintained properly. 

To avoid looking for the predominant species in 377 output jobs manually after modeling, two means are offered At first, a SELECTEDOUTPUT (see also chapter 2.2.1.4) has to be defined in the PHREEQC master input file. Besides pE and pH, it will output all species of interest, for example all Fe species, in a. csv file. These species have to be specified explicitly under the sub key word molalities , e.g. Fe2+, Fe3+, FeOH+, etc. The BASIC-reproduction program inserts the 377 SOLUTION jobs before the key word SELECTED OUTPUT. Since the SOLUTIONS are not separated by an END, a SELECTED OUTPUT will be created out of all SOLUTIONS displaying for each of the 377 jobs a row with the columns pH, pE, m Fe2+ (concentration of Fe2+ in mol/L), m Fe3+, m FeOH+, etc. 

The following example shows how this can be modeled in PHREEQC. First of all, a master- ami a solution species tritium T or T1 have to be defined. Since the input of data for log k und -gamma within the key word SOLUTION SPECIES is required, but unknown, any value can be entered here as a free parameter ( dummy , e g. 0.0). This value is not used for kinetic calculations and thus, does not cause any problems. However, all results based on equilibrium calculations (e.g. the calculation of the saturation index) are nonsense for this species . The tritium values have to be entered in tritium units. However, in order not to have to define or convert them in an extra step, they are entered fictitiously with the unit umol/kgw instead of TU in PHREEQC. As no interactions of tritium with any other species are defined, the unit is eventually irrelevant. After modeling, remember that the result is displayed in mol/kgw as always in PHREEQC and has to be recalculated to the fictitious tritium unit umol/kgw. Entering mol/kgw in the input file, the solution algorithm quits due to problems with too high total ionic strengths. 

The actual task now is to change the PHREEQC job in such a way that the tritium input function is not impulse-like but more realistic. Fig. 43 illustrates the increase of tritium concentrations in precipitation water from 1962 to 1963 and the subsequent decrease from 1963 to 1997, as determined at the climate station Hof-Hohensaas, Germany. 

The acid mine water is defined as SOLUTION 0 and the water in the carbonate channel as SOLUTION 1. Within the key word KINETICS 1-10 the calculation tolerance as well as the initial and the total mole mass of calcite can be defined. Obligatory are only the parameter 50 and 0.6. These are needed by the BASIC program, which must be implemented within the key word RATES. Here, we use the BASIC program listed at the end of the database PHREEQC.dat. If the database PHREEQC.dat is used (which is not free of troubles, since there are, e g., no data for uranium) or if the paragraph is copied into another database, it is not necessary to define a RATES block in the input file. PHREEQC uses automatically the RATES block from the database. Yet, if any other kinetic rates are to be used, the BASIC program must be copied into the input file under RATES. In any case, the KINETICS block is required. 

A summary of the parameters used in the model is provided in Table 3. Dispersivity was determined from breakthrough of nonreactive bromide. Input for PHREEQC requires units of mass per liter of solution. Therefore, concentrations that were directly measured in the solid phase including the mass of solids, and concentrations of Feo.995Aso.oo5(OH)3 and reactive organic... 

Data from the Fe reduction experiment were used to define the As concentration of Fe(OH)3. The PHASES data block of the input file for PHREEQC redefined Fe(OH)3 according to the following reaction ... 

Cation exchange in groundwater is a multicomponent process in which all the solute cations participate. It can be calculated easily with geochemical models such as PHREEQC-2 (Parkhurst and Appelo, 1999) which have databases with representative values of the exchange constants. An example PHREEQC-2 input file for calculating exchangeable iron is given in Table 1. 

Table 1. PHREEQC-2 input file for calculating exchangeable and sorbed iron, and the undimensional distribution coefficient for iron.

The thermodynamic databases that accompany most modeling codes were prepared intentionally to be separate from the codes. This means equilibrium constants are not hard-wired into the codes, which makes it much easier for users to change the values of the equilibrium constants in the database, or add/delete a reaction from the database without affecting the functionality of the codes. Many codes (e.g., phreeqc and EQ3/6) allow users to modify the equilibrium constants in the input file as well as in the database itself (see the Appendix). 

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